1 Analisis of efsa publication on vectors

  • Systematic literature review on the vector status of potential vector species of 36 vector-borne pathogens
  • Information needed for the integration of WG1-WG2
# Library ----
library(readxl)
library(dplyr)
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
library(lubridate)
## 
## Attaching package: 'lubridate'
## The following objects are masked from 'package:base':
## 
##     date, intersect, setdiff, union
library(leaflet)
library(sf)
## Linking to GEOS 3.11.2, GDAL 3.7.2, PROJ 9.3.0; sf_use_s2() is TRUE
library(DT)
library(ggplot2)
setwd("C:/Users/alfredo.acosta/OneDrive - SVA/LORA/Working example/vectors/")

2 DB EfSA

2.1 Reading data

w <- read_xlsx("DL3.1.2.SLR_VectorStatus_Database_comp.xlsx", sheet = 1)

3 Contents of the DB

colnames(w)
##  [1] "ID"                     "First_Author"           "Title"                 
##  [4] "year"                   "Country"                "Region/State"          
##  [7] "City/County"            "Latitude"               "Longitude"             
## [10] "Continent"              "Year_Start"             "Year_End"              
## [13] "Month_Start"            "Month_End"              "Continuous_or_annually"
## [16] "SamplingMethod"         "LifeStage"              "VectorGroup"           
## [19] "VectorSpecies"          "VectorSpeciesOld"       "fedStatus"             
## [22] "Host"                   "anMethCode"             "MethodCategory"        
## [25] "N­Specimens­Tested"     "NPoolsTested"           "Pool_size"             
## [28] "Positive/Negative"      "NPoolspositive"         "VBD_Agent"             
## [31] "VBD_Agent_subtype"      "VBD_AS_Full"            "MIR"                   
## [34] "LCI_MIR"                "UCI_MIR"                "Vectornet_Region"      
## [37] "Trap/Host"              "PrioritySpecies"        "VectornetRegionSpecies"
## [40] "Vndatlocd"              "Vnmaplocd"              "Country_ISO"
table(w$year)
## 
## 1973 1989 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 
##    3  167    4    4   49  134   22   49   58   31  103  395   64   98   78   63 
## 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 
##  112  113  302  298  337  791  653  370  376  657  383   13
table(w$Continent)
## 
##          Africa         Eurasia Eurasia, Africa   North America         Oceania 
##             902            2914              14            1333             250 
##   South America 
##             311
table(w$Host)
## 
##                                                                                              (caught in cow shed) 
##                                                                                                                24 
##                                                                                                    American Robin 
##                                                                                                                 2 
##                                                                                              Anatolian wild sheep 
##                                                                                                                 4 
##                                                                                                    Ardea herodius 
##                                                                                                                 1 
##                                                                                                  Baltimore Oriole 
##                                                                                                                 1 
##                                                                                                              bird 
##                                                                                                                24 
##                                                                                             bird, dog, human, pig 
##                                                                                                                 1 
##                                                                                                             Birds 
##                                                                                                                 6 
##                                                                                             Black-capped chikadee 
##                                                                                                                 1 
##                                                                                                         bloodfed? 
##                                                                                                                 1 
##                                                                                                        Bos taurus 
##                                                                                                                 5 
##                                                                                                            bovine 
##                                                                                                                 2 
##                                                                                                            Bovine 
##                                                                                                                 1 
##                                                                                                       bovine, dog 
##                                                                                                                 1 
##                                                                     Bovine, Dog, barking deer, wild boar, leopard 
##                                                                                                                 1 
##                                                                                   bovine, dog, sambar deer, civet 
##                                                                                                                 1 
##                                                                              bovine, goat, dog,sambar deer, civet 
##                                                                                                                 1 
##                                                                                                     Bubulcus ibis 
##                                                                                                                 1 
##                                                                                                           Buffalo 
##                                                                                                                 1 
##                                                                                                              bull 
##                                                                                                                 4 
##                                                                                                             camel 
##                                                                                                                10 
##                                                                                                             Camel 
##                                                                                                                 3 
##                                                                                                            camels 
##                                                                                                                16 
##                                                                                               Camelus dromedarius 
##                                                                                                                 8 
##                                                                                                       Canis lupus 
##                                                                                                                 2 
##                                                                                            Canis lupus domesticus 
##                                                                                                                 4 
##                                                                                            Canis lupus familiaris 
##                                                                                                                29 
##                                                                                                      Capra hircus 
##                                                                                                                12 
##                                                                                               Capreolus capreolus 
##                                                                                                                 1 
##                                                                                                               cat 
##                                                                                                                 2 
##                                                                                                               Cat 
##                                                                                                                 2 
##                                                                                                            cattle 
##                                                                                                               163 
##                                                                                                            Cattle 
##                                                                                                                23 
##                                                                                      cattle (freshly slaughtered) 
##                                                                                                                26 
##                                                                                                   cattle and goat 
##                                                                                                                 2 
##                                                                                                   cattle and pigs 
##                                                                                                                 3 
##                                                                                                  cattle and sheep 
##                                                                                                                 7 
##                                                                  cattle, domestic and roving dogs, smalls mammals 
##                                                                                                                25 
##                                                                                                     Cattle, goats 
##                                                                                                                 2 
##                                                                                              Cattle, goats, sheep 
##                                                                                                                 4 
##                                                                                        Cattle, goats, sheep, dogs 
##                                                                                                                 7 
##                                                                                   Cattle, goats, sheep, tortoises 
##                                                                                                                 1 
##                                                                           cattle, Lepus europaeus, questing ticks 
##                                                                                                                 2 
##                                                                                        cattle, ruminants, horeses 
##                                                                                                                 2 
##                                                                                                     Cattle, sheep 
##                                                                                                                20 
##                                                                                               cattle, sheep, goat 
##                                                                                                                 6 
##                                                                                              cattle, sheep, goats 
##                                                                                                                28 
## cattle, sheep, horse, Lepus europaeus, man, questing ticks, Lepus europaeus, Corvus frugilegus, Galerida cristata 
##                                                                                                                 2 
##                                                                                                 Cattle, tortoises 
##                                                                                                                 1 
##                                                                                                           cattles 
##                                                                                                                 3 
##                                                                                         Cervus elaphus hispanicus 
##                                                                                                                 3 
##                                                                                                          Chickens 
##                                                                                                                 1 
##                                                                                             Chrysocyon brachyurus 
##                                                                                                                 1 
##                                                                                               Common Yellowthroat 
##                                                                                                                 2 
##                                                                                                               cow 
##                                                                                                                 7 
##                                                                                                               Cow 
##                                                                                                                12 
##                                                                                                     cow, dog, pig 
##                                                                                                                 1 
##                                                                                              cow, dog, sheep, pig 
##                                                                                                                 1 
##                                                                                                  cow, sheep, goat 
##                                                                                                                 6 
##                                                                                                              crow 
##                                                                                                                 1 
##                                                                                                              deer 
##                                                                                                                30 
##                                                                                                        deer, boar 
##                                                                                                                 1 
##                                                                                                               dog 
##                                                                                                                19 
##                                                                                                               Dog 
##                                                                                                                 9 
##                                                                                                        Dog, sheep 
##                                                                                                                 2 
##                                                                                                 Dog, sheep, goats 
##                                                                                                                 2 
##                                                                                                              dogs 
##                                                                                                                 2 
##                                                                                                dogs, cats, horses 
##                                                                                                               218 
##                                                                                                domestic ruminants 
##                                                                                                                 1 
##                                                                                                            donkey 
##                                                                                                                 1 
##                                                                                    Donkey, goat, camel and others 
##                                                                                                                 1 
##                                                                                                    Eastern Towhee 
##                                                                                                                 1 
##                                                                                                    Ergretta thula 
##                                                                                                                 1 
##                                                                                                       fallow deer 
##                                                                                                                 3 
##                                                                                                      Farm animals 
##                                                                                                                 1 
##                                                                                                       Felis catus 
##                                                                                                                 1 
##                                                                flagging, dog, hedgehog, european badger, tortoise 
##                                                                                                                 3 
##                                                                                                               fox 
##                                                                                                                 1 
##                                                                                                              goat 
##                                                                                                                18 
##                                                                                                              Goat 
##                                                                                                                10 
##                                                                                                       goat, sheep 
##                                                                                                                21 
##                                                                                                       Goat, sheep 
##                                                                                                                 1 
##                                                                                                             goats 
##                                                                                                                 8 
##                                                                                     goats, sheep, cattle, buffalo 
##                                                                                                                 8 
##                                                                                            greek tortoise, camels 
##                                                                                                                 2 
##                                                                                                   ground squirrel 
##                                                                                                                 1 
##                                                                                                      Guinea fowls 
##                                                                                                                 2 
##                                                                                                              hare 
##                                                                                                                 5 
##                                                                                                             Hares 
##                                                                                                                 1 
##                                                                                                          hedgehog 
##                                                                                                                 4 
##                                                                                                      Homo sapiens 
##                                                                                                                15 
##                                                                                                        House Wren 
##                                                                                                                 1 
##                                                                                                             human 
##                                                                                                                17 
##                                                                                                             Human 
##                                                                                                                 8 
##                                                                                                       human, bird 
##                                                                                                                 1 
##                                                               Human, cattle, sheep, goat, unidentified and others 
##                                                                                                                 1 
##                                                                                         Hydrochoerus hydrochaeris 
##                                                                                                                 1 
##                                                                                                    Indigo Bunting 
##                                                                                                                 1 
##                                                                                              Indotestudo elongata 
##                                                                                                                 2 
##                                                                                                 Lincoln's Sparrow 
##                                                                                                                 1 
##                                                                                                  livestock, sheep 
##                                                                                                                 4 
##                                                                                                lon-legged buzzard 
##                                                                                                                 1 
##                                                                                                       Meles meles 
##                                                                                                                 1 
##                                                                                                   Migratory birds 
##                                                                                                                 2 
##                                                                                                   Monitor lizards 
##                                                                                                                 1 
##                                                                                                mouflon, wild boar 
##                                                                                                                 1 
##                                                                                                                NA 
##                                                                                                              2464 
##                                                                                                              None 
##                                                                                                                19 
##                                                                                          North American porcupine 
##                                                                                                                 1 
##                                                                                              Northern Waterthrush 
##                                                                                                                 1 
##                                                                                                          Ovenbird 
##                                                                                                                 1 
##                                                                                                        Ovis aries 
##                                                                                                                 5 
##                                                                                                                ox 
##                                                                                                                32 
##                                                                                                         partridge 
##                                                                                                                 1 
##                                                                                                 Passer domesticus 
##                                                                                                                 1 
##                                                                                         Pelecanus erythrorhunchos 
##                                                                                                                 1 
##                                                                                            pig, dog, human, sheep 
##                                                                                                                 1 
##                                                                                                           Poultry 
##                                                                                                                 1 
##                                                                                                            python 
##                                                                                                                 1 
##                                                                                                     questing tick 
##                                                                                                                 3 
##                                                                                                          red deer 
##                                                                                                                 2 
##                                                                                            Red deer and wild boar 
##                                                                                                                 2 
##                                                                                               red deer, wild boar 
##                                                                                                                 2 
##                                                                                                       sambar deer 
##                                                                                                                 2 
##                                                                                                              shee 
##                                                                                                                 1 
##                                                                                                             sheep 
##                                                                                                                66 
##                                                                                                             Sheep 
##                                                                                                                37 
##                                                                                                     Sheep, bovine 
##                                                                                                                 2 
##                                                                                                     sheep, cattle 
##                                                                                                                 1 
##                                                                                               sheep, cattle, goat 
##                                                                                                                 5 
##                                                                                              sheep, cattle, goats 
##                                                                                                                 5 
##                                                                                                       sheep, goat 
##                                                                                                                 8 
##                                                                                                       Sheep, goat 
##                                                                                                                 1 
##                                                                                         Sheep, goat, unidentified 
##                                                                                                                 1 
##                                                                                                     sheep, humans 
##                                                                                                                 1 
##                                                                                                         Sika deer 
##                                                                                                                 4 
##                                                                                                      Song Sparrow 
##                                                                                                                 1 
##                                                                                                        Sus scrofa 
##                                                                                                                 2 
##                                                                                                    Testudo graeca 
##                                                                                                                 1 
##                                                                                                          tortoise 
##                                                                                                                 2 
##                                                                                                         Tortoises 
##                                                                                                                 2 
##                                                                                                Turdus migratorius 
##                                                                                                                 1 
##                                                                                                            Turkey 
##                                                                                                                 1 
##                                                                                                           unclear 
##                                                                                                               815 
##                                                                                                      Urctos arsos 
##                                                                                                                 1 
##                                                                                                             Veery 
##                                                                                                                 1 
##                                                                                                     Vulpes vulpes 
##                                                                                                                 7 
##                                                                                                   warthog burrows 
##                                                                                                                 5 
##                                                                                                         wild boar 
##                                                                                                                 6 
##                                                                                                         Wild boar 
##                                                                                                                 9 
##                                                                                               yellow legged gulls 
##                                                                                                                 1
table(w$VBD_AS_Full)
## 
##           African horse sickness virus              African swine fever virus 
##                                     27                                    239 
##                          Akabane virus      Alkhurma haemorrhagic fever virus 
##                                     21                                     13 
##                       Bluetongue virus                     Cache Valley virus 
##                                    266                                    120 
## Crimean-Congo haemorrhagic fever virus      Eastern equine encephalitis virus 
##                                    637                                    118 
##                  Ehrlichia ruminantium    Epizootic hemorrhagic disease virus 
##                                    197                                     79 
##              Equine encephalosis virus                            Getah virus 
##                                     20                                     44 
##                       Hepatozoon canis            Japanese encephalitis virus 
##                                    534                                    437 
##                    Leishmania infantum                Rift Valley fever virus 
##                                    567                                    101 
##                    Schmallenberg virus                            Shuni virus 
##                                    262                                     10 
##           St. Louis encephalitis virus                          Thogoto virus 
##                                     46                                      1 
##   Venezuelan equine encephalitis virus   Vesicular stomatitis - Indiana virus 
##                                     10                                     13 
##                      Wesselsbron virus                        West Nile virus 
##                                      6                                   1927 
##      Western equine encephalitis virus                       Yunnan orbivirus 
##                                     12                                     20
table(w$VBD_Agent_subtype)
## 
##  AHFV  AHSV  AKAV  ASFV   BTV  CanL CCHFV cowdr Cowdr   CVV  EEEV   EEV  EHDV 
##    13    27    21   239   266   567   637    23   174   120   118    20    79 
##  GETV hepat   JEV  RVFV   SBV  SHUV  SLEV  THOV  VEEV  VSIV  WEEV   WNV  WSLV 
##    44   534   437   101   262    10    46     1    10    13    12  1927     6 
##  YUOV 
##    20
table(w$VBD_Agent_subtype)
## 
##  AHFV  AHSV  AKAV  ASFV   BTV  CanL CCHFV cowdr Cowdr   CVV  EEEV   EEV  EHDV 
##    13    27    21   239   266   567   637    23   174   120   118    20    79 
##  GETV hepat   JEV  RVFV   SBV  SHUV  SLEV  THOV  VEEV  VSIV  WEEV   WNV  WSLV 
##    44   534   437   101   262    10    46     1    10    13    12  1927     6 
##  YUOV 
##    20
table(w$VectorGroup)
## 
## Biting midges    mosquitoes    Mosquitoes    Sand flies         Ticks 
##           715             6          2813           557          1636
table(w$VectorSpecies)
## 
##                                             Aedeomyia furfurea 
##                                                              3 
##                                        Aedeomyia madagascarica 
##                                                              3 
##                                         Aedeomyia squamipennis 
##                                                              2 
##                                               Aedes abserratus 
##                                                              6 
##                                       Aedes abserratus/punctor 
##                                                              2 
##                                                  Aedes aegypti 
##                                                             21 
##                                             Aedes albodorsalis 
##                                                              1 
##                                            Aedes albolateralis 
##                                                              1 
##                                               Aedes albopictus 
##                                                            134 
##                                               Aedes albothorax 
##                                                              1 
##                                             Aedes andamanensis 
##                                                              1 
##                                               Aedes annandalei 
##                                                              6 
##                                                Aedes annulipes 
##                                                              3 
##                                        Aedes argenteopunctatus 
##                                                              1 
##                                               Aedes atlanticus 
##                                                              2 
##                                     Aedes atlanticus/tormentor 
##                                                              3 
##                                               Aedes atropalpus 
##                                                              1 
##                                                  Aedes aurifer 
##                                                              6 
##                                                 Aedes caballus 
##                                                              2 
##                                               Aedes canadensis 
##                                                             19 
##                                                  Aedes cantans 
##                                                              7 
##                                                 Aedes cantator 
##                                                             14 
##                                                  Aedes caspius 
##                                                             92 
##                                                 Aedes cinereus 
##                                                             29 
##                                         Aedes cinereus/geminus 
##                                                              6 
##                                           Aedes circumluteolus 
##                                                              3 
##                                                 Aedes communis 
##                                                              6 
##                                           Aedes communis group 
##                                                              2 
##                                             Aedes culiciformis 
##                                                              1 
##                                                Aedes cumminsii 
##                                                              4 
##                                                 Aedes dalzieli 
##                                                              3 
##                                                 Aedes dentatus 
##                                                              2 
##                                                 Aedes detritus 
##                                                              8 
##                                               Aedes domesticus 
##                                                              1 
##                                                 Aedes dorsalis 
##                                                             10 
##                                              Aedes durbanensis 
##                                                              2 
##                                               Aedes excrucians 
##                                                              8 
##                                                  Aedes fitchii 
##                                                              2 
##                                               Aedes flavescens 
##                                                              5 
##                                           Aedes fulvus pallens 
##                                                              1 
##                                                 Aedes furcifer 
##                                                              1 
##                                               Aedes geniculata 
##                                                              3 
##                                              Aedes geniculatus 
##                                                             14 
##                                                 Aedes gibbinsi 
##                                                              4 
##                                               Aedes grossbecki 
##                                                              3 
##                                               Aedes hendersoni 
##                                                              2 
##                                                 Aedes hirsutus 
##                                                              1 
##                                               Aedes increpitus 
##                                                              1 
##                                                  Aedes ingrami 
##                                                              2 
##                                                Aedes intrudens 
##                                                              2 
##                                                Aedes japonicus 
##                                                             28 
##                                            Aedes katherinensis 
##                                                              1 
##                                                    Aedes kochi 
##                                                              1 
##                                                 Aedes koreicus 
##                                                              2 
##                                             Aedes littlechildi 
##                                                              1 
##                                            Aedes luteocephalus 
##                                                              1 
##                                             Aedes maculipennis 
##                                                              3 
##                                                Aedes mcintoshi 
##                                                              2 
##                                            Aedes mediovittatus 
##                                                              1 
##                                                Aedes melanimon 
##                                                              3 
##                                               Aedes metallicus 
##                                                              1 
##                                                  Aedes minimus 
##                                                              3 
##                                             Aedes nigromaculis 
##                                                              1 
##                                             Aedes notoscriptus 
##                                                              2 
##                                                Aedes ochraceus 
##                                                              6 
##                                              Aedes penghuensis 
##                                                              2 
##                                               Aedes phylolabis 
##                                                              1 
##                                             Aedes pulcritarsis 
##                                                              2 
##                                                 Aedes rossicus 
##                                                              6 
##                                                 Aedes rusticus 
##                                                              1 
##                                               Aedes scapularis 
##                                                              2 
##                                              Aedes scutellaris 
##                                                              1 
##                                                 Aedes serratus 
##                                                              1 
##                                                 Aedes simpsoni 
##                                                              1 
##                                              Aedes sollicitans 
##                                                             18 
##                                                 Aedes spenceri 
##                                                              1 
##                                                Aedes sticticus 
##                                                             13 
##                                                Aedes stimulans 
##                                                             14 
##                                          Aedes stimulans group 
##                                                              4 
##                                                Aedes stoneorum 
##                                                              1 
##                                             Aedes subargenteus 
##                                                              1 
##                                               Aedes sudanensis 
##                                                              1 
##                                           Aedes taeniorhynchus 
##                                                             20 
##                                                 Aedes tarsalis 
##                                                              1 
##                                                Aedes thibaulti 
##                                                              4 
##                                                    Aedes togoi 
##                                                              2 
##                                                 Aedes tortilis 
##                                                              1 
##                                                 Aedes tremulus 
##                                                              1 
##                                              Aedes tricholabis 
##                                                              6 
##                                                Aedes trichuris 
##                                                              2 
##                                              Aedes triseriatus 
##                                                             33 
##                                   Aedes triseriatus/hendersoni 
##                                                              1 
##                                              Aedes trivittatus 
##                                                             24 
##                                                   Aedes vexans 
##                                                             93 
##                                        Aedes vexans arabiensis 
##                                                              6 
##                                          Aedes vexans nipponii 
##                                                              1 
##                                         Aedes vexans nocturnus 
##                                                              1 
##                                              Aedes vexans s.l. 
##                                                              1 
##                                                  Aedes vigilax 
##                                                              1 
##                                                 Aedes vittatus 
##                                                              1 
##                                          Amblyomma brasiliense 
##                                                              1 
##                                           Amblyomma cajennense 
##                                                              2 
##                                            Amblyomma cohaerens 
##                                                              3 
##                                             Amblyomma detritum 
##                                                              2 
##                                            Amblyomma dubitatum 
##                                                              2 
##                                       Amblyomma falsomarmoreum 
##                                                              1 
##                                                Amblyomma gemma 
##                                                              6 
##                                            Amblyomma geoemydae 
##                                                              2 
##                                             Amblyomma gervaisi 
##                                                              1 
##                                             Amblyomma hebraeum 
##                                                             42 
##                                             Amblyomma integrum 
##                                                              1 
##                                                Amblyomma latum 
##                                                              1 
##                                              Amblyomma lepidum 
##                                                              7 
##                                            Amblyomma marmoreum 
##                                                              2 
##                                              Amblyomma nutalli 
##                                                              1 
##                                               Amblyomma parvum 
##                                                              1 
##                                             Amblyomma sculptum 
##                                                              2 
##                                              Amblyomma sparsum 
##                                                              1 
##                                        Amblyomma testudinarium 
##                                                              8 
##                                             Amblyomma tigrinum 
##                                                              1 
##                              Amblyomma triguttatum triguttatum 
##                                                             11 
##                                           Amblyomma variegatum 
##                                                            101 
##                                            Anopheles albimanus 
##                                                              2 
##                                          Anopheles algeriensis 
##                                                              2 
##                                            Anopheles annulipes 
##                                                              1 
##                                                Anopheles apoci 
##                                                              1 
##                                            Anopheles aquasalis 
##                                                              2 
##                                           Anopheles atroparvus 
##                                                              2 
##                                              Anopheles atropos 
##                                                              5 
##                                              Anopheles barberi 
##                                                              7 
##                                         Anopheles barbirostris 
##                                                              4 
##                                             Anopheles claviger 
##                                                             11 
##                                  Anopheles claviger/petragnani 
##                                                              4 
##                                             Anopheles coustani 
##                                                              6 
##                                             Anopheles crucians 
##                                                              9 
##                                        Anopheles crucians s.l. 
##                                                              2 
##                                               Anopheles dthali 
##                                                              2 
##                                         Anopheles farauti s.l. 
##                                                              1 
##                                          Anopheles fluviatilis 
##                                                              2 
##                                         Anopheles franciscanus 
##                                                              4 
##                                            Anopheles freeborni 
##                                                              4 
##                                             Anopheles funestus 
##                                                              4 
##                                              Anopheles gambiae 
##                                                              6 
##                                            Anopheles grabhamii 
##                                                              1 
##                                               Anopheles hermsi 
##                                                              2 
##                                                Anopheles hilli 
##                                                              1 
##                                             Anopheles hyrcanus 
##                                                              6 
##                                             Anopheles implexus 
##                                                              3 
##                                                Anopheles kochi 
##                                                              3 
##                                         Anopheles kunmingensis 
##                                                              3 
##                                             Anopheles ludlowae 
##                                                              1 
##                                         Anopheles maculipalpis 
##                                                              2 
##                                         Anopheles maculipennis 
##                                                             31 
##                                   Anopheles maculipennis group 
##                                                              2 
##                                    Anopheles maculipennis s.l. 
##                                                             21 
##                                              Anopheles marteri 
##                                                              1 
##                                          Anopheles mascarensis 
##                                                              1 
##                                              Anopheles messeae 
##                                                              3 
##                                              Anopheles minimus 
##                                                              3 
##                                           Anopheles multicolor 
##                                                              1 
##                                      Anopheles neomaculipalpus 
##                                                              2 
##                                             Anopheles pauliani 
##                                                              3 
##                                        Anopheles peditaeniatus 
##                                                              3 
##                                           Anopheles pharoensis 
##                                                              6 
##                                             Anopheles plumbeus 
##                                                             15 
##                                         Anopheles pseudopictus 
##                                                              3 
##                                         Anopheles punctipennis 
##                                                             23 
##                                      Anopheles quadrimaculatus 
##                                                             28 
##                                 Anopheles quadrimaculatus s.l. 
##                                                              2 
##                                              Anopheles rufipes 
##                                                              7 
##                                            Anopheles sacharovi 
##                                                              1 
##                                            Anopheles sergentii 
##                                                              1 
##                                             Anopheles sinensis 
##                                                             18 
##                                            Anopheles squamosus 
##                                                              2 
##                                   Anopheles squamosus/cydippis 
##                                                              3 
##                                            Anopheles stephensi 
##                                                              2 
##                                            Anopheles subpictus 
##                                                             22 
##                                          Anopheles superpictus 
##                                                              4 
##                                           Anopheles tenebrosus 
##                                                              3 
##                                          Anopheles tessellatus 
##                                                              9 
##                                                Anopheles vagus 
##                                                              4 
##                                        Anopheles vestitipennis 
##                                                              2 
##                                              Anopheles walkeri 
##                                                             11 
##                                             Anopheles ziemanni 
##                                                              1 
##                                                 Argas persicus 
##                                                              2 
##                                                 Argas reflexus 
##                                                              1 
##                                                 Argas vulgaris 
##                                                              2 
##                                           Armigeres subalbatus 
##                                                             17 
##                                   Bichromomyia flaviscutellata 
##                                                              4 
##                                     Bichromomyia olmeca olmeca 
##                                                              3 
##                                            Boophilus annulatus 
##                                                              3 
##                                            Boophilus decoratus 
##                                                              1 
##                                           Brumptomyia avellari 
##                                                              2 
##                                             Brumptomyia hamata 
##                                                              1 
##                                              Brumptomyia mesai 
##                                                              1 
##                                        Brumptomyia nitzulescui 
##                                                              1 
##                                         Coquillettidia aurites 
##                                                              3 
##                                       Coquillettidia crassipes 
##                                                              3 
##                                         Coquillettidia fraseri 
##                                                              1 
##                                    Coquillettidia fuscopennata 
##                                                              3 
##                                       Coquillettidia metallica 
##                                                              4 
##                                       Coquillettidia nigricans 
##                                                              1 
##                                        Coquillettidia ochracea 
##                                                              2 
##                                        Coquillettidia Ochracea 
##                                                              1 
##                                      Coquillettidia perturbans 
##                                                             35 
##                                   Coquillettidia pseudoconopas 
##                                                              1 
##                                      Coquillettidia richiardii 
##                                                             17 
##                                   Coquillettidia venezuelensis 
##                                                              1 
##                                      Coquillettidia versicolor 
##                                                              2 
##                                               Culex adersianus 
##                                                              1 
##                                                Culex annulatus 
##                                                              1 
##                                               Culex annulioris 
##                                                              4 
##                                                  Culex annulus 
##                                                             16 
##                                               Culex antennatus 
##                                                             12 
##                                                  Culex atratus 
##                                                              2 
##                                               Culex bahamensis 
##                                                              2 
##                                          Culex bidens/interfor 
##                                                              1 
##                                         Culex bitaeniorhynchus 
##                                                             13 
##                                                  Culex boharti 
##                                                              1 
##                                              Culex brevipalpis 
##                                                              1 
##                                                  Culex cedecei 
##                                                              2 
##                                               Culex chidesteri 
##                                                              1 
##                                                Culex coronator 
##                                                              2 
##                                                   Culex decens 
##                                                              5 
##                                                  Culex duttoni 
##                                                              1 
##                                                Culex erraticus 
##                                                             23 
##                                            Culex erythrothorax 
##                                                             17 
##                                                 Culex fuscanus 
##                                                              3 
##                                             Culex fuscocephala 
##                                                             22 
##                                                  Culex gelidus 
##                                                             23 
##                                              Culex habilitator 
##                                                              1 
##                                                Culex hortensis 
##                                                              5 
##                                                Culex impudicus 
##                                                              2 
##                                                 Culex inatomii 
##                                                              1 
##                                                   Culex infula 
##                                                              2 
##                                             Culex interrogator 
##                                                              1 
##                                                Culex iolambdis 
##                                                              1 
##                                                  Culex janitor 
##                                                              1 
##                                              Culex laticinctus 
##                                                              1 
##                                                 Culex martinii 
##                                                              2 
##                                                Culex mimeticus 
##                                                              5 
##                                                 Culex modestus 
##                                                             32 
##                                                 Culex murrelli 
##                                                              3 
##                                                   Culex neavei 
##                                                             10 
##                                                Culex nebulosus 
##                                                              1 
##                                              Culex nigripalpus 
##                                                             13 
##                                           Culex nigropunctatus 
##                                                              1 
##                                               Culex opisthopus 
##                                                              1 
##                                               Culex orientalis 
##                                                              2 
##                                                   Culex pedroi 
##                                                              1 
##                                               Culex perexiguus 
##                                                              9 
##                                                Culex perfuscus 
##                                                              4 
##                                                  Culex pipiens 
##                                                            317 
##                                 Culex pipiens biotype molestus 
##                                                              2 
##                                  Culex pipiens biotype pipiens 
##                                                              7 
## Culex pipiens biotype pipiens x Culex pipiens biotype molestus 
##                                                              1 
##                                          Culex pipiens pallens 
##                                                              4 
##                                             Culex pipiens s.l. 
##                                                             65 
##                         Culex pipiens x Culex quinquefasciatus 
##                                                              5 
##                                         Culex pipiens/restuans 
##                                                             47 
##                                       Culex pipiens/torrentium 
##                                                              2 
##                                               Culex poicilipes 
##                                                             13 
##                                            Culex pseudovishnui 
##                                                             17 
##                                                 Culex pusillus 
##                                                              2 
##                                         Culex quinquefasciatus 
##                                                            105 
##                                                 Culex restuans 
##                                                             55 
##                                                     Culex rima 
##                                                              1 
##                                                Culex rubinotus 
##                                                              1 
##                                             Culex rubithoracis 
##                                                              5 
##                                               Culex salinarius 
##                                                             31 
##                                                 Culex simpsoni 
##                                                              1 
##                                                 Culex sinensis 
##                                                              1 
##                                                  Culex sitiens 
##                                                              4 
##                                            Culex sitiens group 
##                                                              3 
##                                         Culex sitiens subgroup 
##                                                              8 
##                                                 Culex spinosus 
##                                                              1 
##                                             Culex stigmatosoma 
##                                                              6 
##                                               Culex striatipes 
##                                                              1 
##                                                Culex taeniopus 
##                                                              1 
##                                                 Culex tarsalis 
##                                                             90 
##                                                Culex territans 
##                                                             28 
##                                                   Culex terzii 
##                                                              1 
##                                                 Culex theileri 
##                                                             26 
##                                                Culex thriambus 
##                                                              6 
##                                                 Culex tigripes 
##                                                              1 
##                                               Culex torrentium 
##                                                              3 
##                                               Culex trifilatus 
##                                                              2 
##                                        Culex tritaeniorhynchus 
##                                                            148 
##                                              Culex univittatus 
##                                                             16 
##                                                   Culex vagans 
##                                                              3 
##                                              Culex vansomereni 
##                                                              1 
##                                                  Culex vicinus 
##                                                              1 
##                                                  Culex vishnui 
##                                                             19 
##                                         Culex vishnui subgroup 
##                                                              2 
##                                                    Culex watti 
##                                                              1 
##                                                Culex whitmorei 
##                                                             11 
##                                               Culex zombaensis 
##                                                              2 
##                                             Culicoides achrayi 
##                                                              4 
##                                              Culicoides actoni 
##                                                              2 
##                                          Culicoides alazanicus 
##                                                              2 
##                                            Culicoides arakawae 
##                                                             10 
##                                            Culicoides arakawai 
##                                                              1 
##                                          Culicoides arboricola 
##                                                              4 
##                                        Culicoides badooshennis 
##                                                              1 
##                                              Culicoides baueri 
##                                                              2 
##                                             Culicoides begueti 
##                                                              1 
##                                            Culicoides bickleyi 
##                                                              1 
##                                          Culicoides biguttatus 
##                                                              2 
##                                          Culicoides brunnicans 
##                                                              1 
##                                Culicoides cataneii/gejgelensis 
##                                                              2 
##                                          Culicoides chiopterus 
##                                                             16 
##                                      Culicoides circumscriptus 
##                                                              7 
##                                          Culicoides clastrieri 
##                                                              2 
##                                       Culicoides crepuscularis 
##                                                             11 
##                                         Culicoides cylindratus 
##                                                              2 
##                                        Culicoides debilipalpis 
##                                                             12 
##                                              Culicoides deltus 
##                                                              2 
##                                         Culicoides dendriticus 
##                                                              1 
##                                             Culicoides dewulfi 
##                                                             22 
##                                        Culicoides duddingstoni 
##                                                              1 
##                                            Culicoides fagineus 
##                                                              2 
##                                         Culicoides fascipennis 
##                                                              3 
##                                       Culicoides festivipennis 
##                                                              6 
##                                      Culicoides flavipulicaris 
##                                                              7 
##                                              Culicoides fulvus 
##                                                              4 
##                                         Culicoides furcillatus 
##                                                              1 
##                                              Culicoides furens 
##                                                              1 
##                                         Culicoides gejgelensis 
##                                                              2 
##                                        Culicoides griseidorsum 
##                                                              1 
##                                          Culicoides grisescens 
##                                                              1 
##                                            Culicoides guttifer 
##                                                              1 
##                                         Culicoides guttipennis 
##                                                              2 
##                                        Culicoides haematopotus 
##                                                             12 
##                                             Culicoides haranti 
##                                                              1 
##                                         Culicoides heliophilus 
##                                                              1 
##                                             Culicoides hinmani 
##                                                              1 
##                                           Culicoides homotomus 
##                                                              4 
##                                           Culicoides humeralis 
##                                                              2 
##                                             Culicoides imicola 
##                                                             43 
##                                        Culicoides imicola s.l. 
##                                                              3 
##                                   Culicoides imicola/bolitinos 
##                                                              1 
##                                         Culicoides impunctatus 
##                                                              2 
##                                       Culicoides insignipennis 
##                                                              1 
##                                            Culicoides insignis 
##                                                              4 
##                                           Culicoides jacobsoni 
##                                                              3 
##                                          Culicoides kibunensis 
##                                                              1 
##                                                Culicoides liui 
##                                                              1 
##                                         Culicoides longipennis 
##                                                              3 
##                                        Culicoides lungchiensis 
##                                                              2 
##                                           Culicoides lupicaris 
##                                                              2 
##                                           Culicoides maritimus 
##                                                              3 
##                                          Culicoides matsuzawai 
##                                                              2 
##                                        Culicoides minutissimus 
##                                                              1 
##                                    Culicoides mississippiensis 
##                                                              1 
##                                               Culicoides nanus 
##                                                              2 
##                                           Culicoides newsteadi 
##                                                             31 
##                                   Culicoides newsteadi complex 
##                                                              2 
##                                     Culicoides newsteadi group 
##                                                              4 
##                                      Culicoides newsteadi s.l. 
##                                                              1 
##                                         Culicoides nipponensis 
##                                                             20 
##                                         Culicoides nubeculosus 
##                                                              6 
##                                    Culicoides nubeculosus s.l. 
##                                                             14 
##                                   Culicoides obsoletus complex 
##                                                            103 
##                                     Culicoides obsoletus group 
##                                                             10 
##                                      Culicoides obsoletus s.l. 
##                                                             24 
##                                Culicoides obsoletus/sanguisuga 
##                                                              1 
##                                             Culicoides odiatus 
##                                                              1 
##                                            Culicoides odibilis 
##                                                              1 
##                                             Culicoides ohmorii 
##                                                              2 
##                                          Culicoides orientalis 
##                                                             15 
##                                            Culicoides oxystoma 
##                                                             26 
##                                       Culicoides pallidicornis 
##                                                              2 
##                                              Culicoides paolae 
##                                                              1 
##                                           Culicoides paraensis 
##                                                              1 
##                                             Culicoides parroti 
##                                                              2 
##                                          Culicoides peregrinus 
##                                                             11 
##                                         Culicoides pictipennis 
##                                                              1 
##                                          Culicoides picturatus 
##                                                              1 
##                                      Culicoides poperinghensis 
##                                                              1 
##                                           Culicoides pulicaris 
##                                                             44 
##                                     Culicoides pulicaris group 
##                                                              7 
##                                      Culicoides pulicaris s.l. 
##                                                             21 
##                                 Culicoides pulicaris/lupicaris 
##                                                              1 
##                                           Culicoides punctatus 
##                                                             43 
##                                        Culicoides puncticollis 
##                                                              3 
##                                            Culicoides pusillus 
##                                                              2 
##                                          Culicoides reconditus 
##                                                              1 
##                                              Culicoides riethi 
##                                                              1 
##                                              Culicoides riouxi 
##                                                              1 
##                                          Culicoides salinarius 
##                                                              2 
##                                          Culicoides santonicus 
##                                                              1 
##                                            Culicoides scanloni 
##                                                              1 
##                                      Culicoides schultzei s.l. 
##                                                              3 
##                                            Culicoides scoticus 
##                                                              4 
##                                              Culicoides segnis 
##                                                              1 
##                                 Culicoides sejfadinei/tauricus 
##                                                              1 
##                                        Culicoides shaklawensis 
##                                                              1 
##                                           Culicoides simulator 
##                                                              1 
##                                          Culicoides sonorensis 
##                                                             11 
##                                            Culicoides spiculae 
##                                                              1 
##                                            Culicoides spinosus 
##                                                              3 
##                                           Culicoides stellifer 
##                                                             14 
##                                              Culicoides stigma 
##                                                              1 
##                                         Culicoides subfagineus 
##                                                              1 
##                                     Culicoides subfasciipennis 
##                                                              3 
##                                            Culicoides sumatrae 
##                                                              2 
##                                            Culicoides tagineus 
##                                                              1 
##                                            Culicoides tainanus 
##                                                              4 
##                                            Culicoides torreyae 
##                                                              1 
##                                            Culicoides venustus 
##                                                             13 
##                                              Culicoides vexans 
##                                                              1 
##                                       Culicoides villosipennis 
##                                                              2 
##                                           Culiseta alaskaensis 
##                                                              1 
##                                              Culiseta annulata 
##                                                             23 
##                                             Culiseta impatiens 
##                                                              1 
##                                              Culiseta incidens 
##                                                              7 
##                                              Culiseta inornata 
##                                                             16 
##                                         Culiseta longiareolata 
##                                                             24 
##                                              Culiseta melanura 
##                                                             70 
##                                            Culiseta minnesotae 
##                                                              6 
##                                             Culiseta morsitans 
##                                                              7 
##                                             Culiseta particeps 
##                                                              1 
##                                             Culiseta subochrea 
##                                                              3 
##                                            Dampfomyia beltrani 
##                                                              4 
##                                            Deinocerites cancer 
##                                                              3 
##                                            Deinocerites magnus 
##                                                              1 
##                                            Dermacentor auratus 
##                                                              1 
##                                         Dermacentor marginatus 
##                                                             44 
##                                             Dermacentor niveus 
##                                                              3 
##                                           Dermacentor nuttalli 
##                                                              4 
##                                       Dermacentor raskenmensis 
##                                                              1 
##                                        Dermacentor reticulatus 
##                                                             11 
##                                           Dermacentor silvarum 
##                                                              2 
##                                             Evandromyia bacula 
##                                                              1 
##                                          Evandromyia bourrouli 
##                                                              1 
##                                         Evandromyia carmelinoi 
##                                                              4 
##                                         Evandromyia cortelezii 
##                                                              7 
##                                    Evandromyia cortelezii s.l. 
##                                                              3 
##                                           Evandromyia edwardsi 
##                                                              3 
##                                           Evandromyia evandroi 
##                                                              4 
##                                              Evandromyia lenti 
##                                                              8 
##                                            Evandromyia sallesi 
##                                                              4 
##                                          Evandromyia saulensis 
##                                                              1 
##                                           Evandromyia spelunca 
##                                                              1 
##                                          Evandromyia teratodes 
##                                                              1 
##                                       Evandromyia termitophila 
##                                                              6 
##                                            Evandromyia walkeri 
##                                                              4 
##                                           Expapillata firmatoi 
##                                                              1 
##                                        Haemagogus mesodentatus 
##                                                              1 
##                                           Haemaphysalis adleri 
##                                                              1 
##                                        Haemaphysalis bancrofti 
##                                                              4 
##                                        Haemaphysalis bispinosa 
##                                                              2 
##                                         Haemaphysalis concinna 
##                                                              8 
##                                         Haemaphysalis erinacei 
##                                                              8 
##                                            Haemaphysalis flava 
##                                                              6 
##                                      Haemaphysalis formosensis 
##                                                              6 
##                                        Haemaphysalis hystricis 
##                                                              3 
##                                          Haemaphysalis inermis 
##                                                              6 
##                                       Haemaphysalis intermedia 
##                                                              1 
##                                         Haemaphysalis kitaokai 
##                                                              3 
##                                      Haemaphysalis lagostrophi 
##                                                              1 
##                                           Haemaphysalis leachi 
##                                                              2 
##                                      Haemaphysalis longicornis 
##                                                             31 
##                                            Haemaphysalis parva 
##                                                             27 
##                                         Haemaphysalis punctata 
##                                                             22 
##                                     Haemaphysalis qinghaiensis 
##                                                              1 
##                                          Haemaphysalis shimoga 
##                                                              1 
##                                        Haemaphysalis spinigera 
##                                                              1 
##                                          Haemaphysalis sulcata 
##                                                             21 
##                                             Hyalomma aegyptium 
##                                                             15 
##                                            Hyalomma anatolicum 
##                                                             55 
##                                 Hyalomma anatolicum anatolicum 
##                                                              1 
##                                             Hyalomma asiaticum 
##                                                             29 
##                                   Hyalomma asiaticum asiaticum 
##                                                              3 
##                                              Hyalomma detritum 
##                                                              9 
##                                            Hyalomma dromedarii 
##                                                             34 
##                                             Hyalomma excavatum 
##                                                             28 
##                                               Hyalomma glabrum 
##                                                              1 
##                                            Hyalomma impeltatum 
##                                                              9 
##                                             Hyalomma impressum 
##                                                              4 
##                                           Hyalomma lusitanicum 
##                                                             36 
##                                            Hyalomma marginatum 
##                                                             86 
##                                    Hyalomma marginatum rufipes 
##                                                              2 
##                                             Hyalomma marmoreum 
##                                                              2 
##                                               Hyalomma rufipes 
##                                                             12 
##                                     Hyalomma rufipes truncatum 
##                                                              1 
##                                              Hyalomma schulzei 
##                                                              3 
##                                              Hyalomma scupense 
##                                                             14 
##                                             Hyalomma truncatum 
##                                                             16 
##                                             Hyalomma turanicum 
##                                                              2 
##                                               Ixodes cornuatus 
##                                                              5 
##                                              Ixodes crenulatus 
##                                                              2 
##                                               Ixodes frontalis 
##                                                              2 
##                                                Ixodes gibbosus 
##                                                              1 
##                                               Ixodes hexagonus 
##                                                              4 
##                                                  Ixodes hirsti 
##                                                              1 
##                                              Ixodes holocyclus 
##                                                             84 
##                                              Ixodes inopinatus 
##                                                              2 
##                                                  Ixodes laguri 
##                                                              1 
##                                              Ixodes myrmecobii 
##                                                              2 
##                                             Ixodes nipponensis 
##                                                              1 
##                                                  Ixodes ovatus 
##                                                              1 
##                                              Ixodes pavlovskyi 
##                                                              3 
##                                             Ixodes persulcatus 
##                                                              6 
##                                             Ixodes redikorzevi 
##                                                              1 
##                                                 Ixodes ricinus 
##                                                             46 
##                                              Ixodes scapularis 
##                                                             22 
##                                                 Ixodes tasmani 
##                                                             18 
##                                                  Ixodes turdus 
##                                                              1 
##                                               Ixodes ventalloi 
##                                                              2 
##                                                Lutzia tigripes 
##                                                              2 
##                                             Lutzomyia almerioi 
##                                                              3 
##                                             Lutzomyia antunesi 
##                                                              1 
##                                          Lutzomyia cavernicola 
##                                                              2 
##                                     Lutzomyia cortelezzii s.l. 
##                                                              1 
##                                             Lutzomyia cruciata 
##                                                              5 
##                                                Lutzomyia cruzi 
##                                                              1 
##                                             Lutzomyia edwardsi 
##                                                              1 
##                                             Lutzomyia evandroi 
##                                                              1 
##                                             Lutzomyia firmatoi 
##                                                              1 
##                                             Lutzomyia fischeri 
##                                                              1 
##                                      Lutzomyia flaviscutellata 
##                                                              2 
##                                           Lutzomyia forattinii 
##                                                              1 
##                                            Lutzomyia gaminarai 
##                                                              1 
##                                               Lutzomyia gomezi 
##                                                              1 
##                                           Lutzomyia intermedia 
##                                                              1 
##                                                Lutzomyia lenti 
##                                                              1 
##                                               Lutzomyia lloydi 
##                                                              1 
##                                          Lutzomyia longipalpis 
##                                                             82 
##                                          Lutzomyia Longipalpis 
##                                                              9 
##                                              Lutzomyia migonei 
##                                                              2 
##                                               Lutzomyia neivai 
##                                                              1 
##                                                Lutzomyia renei 
##                                                              1 
##                                            Lutzomyia sordellii 
##                                                              1 
##                                           Lutzomyia tupynambai 
##                                                              1 
##                                          Lutzomyia ubiquitalis 
##                                                              1 
##                                           Lutzomyia umbratilis 
##                                                              1 
##                                            Lutzomyia wellcomei 
##                                                              1 
##                                             Lutzomyia whitmani 
##                                                              5 
##                                              Mansonia africana 
##                                                              3 
##                                            Mansonia annulifera 
##                                                              1 
##                                               Mansonia bonneae 
##                                                              1 
##                                                 Mansonia dives 
##                                                              2 
##                                       Mansonia dyari/titillans 
##                                                              1 
##                                              Mansonia flaveola 
##                                                              1 
##                                               Mansonia indiana 
##                                                              2 
##                                             Mansonia nigerrima 
##                                                              3 
##                                             Mansonia titillans 
##                                                              5 
##                                             Mansonia uniformis 
##                                                             24 
##                                            Margaropus winthemi 
##                                                              1 
##                                         Martinsmyia minasensis 
##                                                              1 
##                                          Martinsmyia oliveirai 
##                                                              2 
##                          Micropygomyia cayennensis cayennensis 
##                                                              2 
##                                     Micropygomyia chiapanensis 
##                                                              1 
##                                  Micropygomyia echinatopharynx 
##                                                              1 
##                                       Micropygomyia quinquefer 
##                                                              5 
##                                      Micropygomyia rorotaensis 
##                                                              1 
##                                         Micropygomyia villelai 
##                                                              1 
##                                             Migonemyia migonei 
##                                                              7 
##                                            Mimomyia luzonensis 
##                                                              1 
##                                             Mimomyia splendens 
##                                                              2 
##                                           Nyssomyia intermedia 
##                                                              2 
##                                           Nyssomyia Intermedia 
##                                                              1 
##                                               Nyssomyia neivai 
##                                                              3 
##                                             Nyssomyia whitmani 
##                                                             16 
##                                        Nyssomyia yuilli yuilli 
##                                                              1 
##                                       Ornithodoros canestrinii 
##                                                              1 
##                                         Ornithodoros compactus 
##                                                              2 
##                                     Ornithodoros kalahariensis 
##                                                              1 
##                                         Ornithodoros maritimus 
##                                                              2 
##                                           Ornithodoros moubata 
##                                                              3 
##                                      Ornithodoros moubata s.l. 
##                                                            177 
##                                    Ornithodoros noorsveldensis 
##                                                              1 
##                                      Ornithodoros phacochoerus 
##                                                              2 
##                                          Ornithodoros porcinus 
##                                                             12 
##                               Ornithodoros porcinus domesticus 
##                                                              6 
##                                 Ornithodoros porcinus porcinus 
##                                                              8 
##                                    Ornithodoros waterbergensis 
##                                                              1 
##                                            Ornithodoros zumpti 
##                                                              1 
##                                             Orthopodomyia alba 
##                                                              1 
##                                        Orthopodomyia signifera 
##                                                              5 
##                                          Phlebotomus alexandri 
##                                                              8 
##                                         Phlebotomus anatolicus 
##                                                              1 
##                                         Phlebotomus argentipes 
##                                                             24 
##                                             Phlebotomus ariasi 
##                                                              5 
##                                         Phlebotomus balcanicus 
##                                                              2 
##                                             Phlebotomus brevis 
##                                                              1 
##                                           Phlebotomus chabaudi 
##                                                              2 
##                                           Phlebotomus duboscqi 
##                                                              1 
##                                         Phlebotomus halepensis 
##                                                              2 
##                                          Phlebotomus jacusieli 
##                                                              2 
##                                         Phlebotomus kandelakii 
##                                                              2 
##                                           Phlebotomus killicki 
##                                                              1 
##                                          Phlebotomus langeroni 
##                                                              1 
##                                        Phlebotomus longicuspis 
##                                                             10 
##                                         Phlebotomus major s.l. 
##                                                              6 
##                                          Phlebotomus mascittii 
##                                                              4 
##                                          Phlebotomus neglectus 
##                                                             10 
##                                 Phlebotomus neglectus/syriacus 
##                                                              1 
##                                           Phlebotomus papatasi 
##                                                             52 
##                                         Phlebotomus perfiliewi 
##                                                             13 
##                                        Phlebotomus perniciosus 
##                                                             36 
##                                           Phlebotomus rodhaini 
##                                                              1 
##                                           Phlebotomus sergenti 
##                                                             10 
##                                             Phlebotomus simici 
##                                                              2 
##                                  Phlebotomus simici/halepensis 
##                                                              1 
##                                            Phlebotomus similis 
##                                                              1 
##                                              Phlebotomus tobbi 
##                                                             12 
##                                            Phlebotomus wenyoni 
##                                                              2 
##                                         Pintomyia christenseni 
##                                                              4 
##                                               Pintomyia evansi 
##                                                              2 
##                                             Pintomyia fischeri 
##                                                              4 
##                                          Pintomyia misionensis 
##                                                              1 
##                                            Pintomyia monticola 
##                                                              4 
##                                             Pintomyia ovallesi 
##                                                              1 
##                                              Pintomyia pessoai 
##                                                              3 
##                                                Pressatia choti 
##                                                              1 
##                                        Psathyromyia aclydifera 
##                                                              6 
##                                           Psathyromyia aragaoi 
##                                                              1 
##                                           Psathyromyia baratai 
##                                                              1 
##                                      Psathyromyia bigeniculata 
##                                                              2 
##                                   Psathyromyia campograndensis 
##                                                              1 
##                                        Psathyromyia carpenteri 
##                                                              5 
##                                       Psathyromyia hermanlenti 
##                                                              2 
##                                             Psathyromyia lanei 
##                                                              2 
##                                          Psathyromyia lutziana 
##                                                              3 
##                                          Psathyromyia shannoni 
##                                                              3 
##                                          Psathyromyia undulata 
##                                                              1 
##                                            Psorophora albigenu 
##                                                              1 
##                                             Psorophora ciliata 
##                                                              3 
##                                           Psorophora columbiae 
##                                                              6 
##                                           Psorophora confinnis 
##                                                              2 
##                                          Psorophora cyanescens 
##                                                              1 
##                                               Psorophora ferox 
##                                                             22 
##                                            Psorophora howardii 
##                                                              2 
##                                     Psychodopygus Brasiliensis 
##                                                              1 
##                                           Psychodopygus davisi 
##                                                              2 
##                                         Psychodopygus Lutziana 
##                                                              1 
##                                       Psychodopygus panamensis 
##                                                              6 
##                                        Rhipicephalus annulatus 
##                                                             17 
##                                   Rhipicephalus appendiculatus 
##                                                             13 
##                                        Rhipicephalus australis 
##                                                              2 
##                                            Rhipicephalus bursa 
##                                                             44 
##                                         Rhipicephalus camicasi 
##                                                              2 
##                                      Rhipicephalus decoloratus 
##                                                             28 
##                                          Rhipicephalus evertsi 
##                                                             12 
##                                  Rhipicephalus evertsi evertsi 
##                                                              4 
##                                           Rhipicephalus geigyi 
##                                                              8 
##                                         Rhipicephalus guilhoni 
##                                                              1 
##                                 Rhipicephalus haemaphysaloides 
##                                                              1 
##                                        Rhipicephalus microplus 
##                                                             16 
##                                         Rhipicephalus muhsamae 
##                                                              1 
##                                     Rhipicephalus praetextatus 
##                                                              2 
##                                           Rhipicephalus pravus 
##                                                              2 
##                                       Rhipicephalus pulchellus 
##                                                              5 
##                                          Rhipicephalus pumilio 
##                                                              2 
##                                         Rhipicephalus rossicus 
##                                                              5 
##                                       Rhipicephalus sanguineus 
##                                                            168 
##                                 Rhipicephalus sanguineus group 
##                                                              2 
##                                  Rhipicephalus sanguineus s.l. 
##                                                             40 
##                                         Rhipicephalus schulzei 
##                                                              1 
##                                     Rhipicephalus senegalensis 
##                                                              4 
##                                         Rhipicephalus simpsoni 
##                                                              1 
##                                        Rhipicephalus turanicus 
##                                                             41 
##                                             Sciopemyia microps 
##                                                              1 
##                                           Sciopemyia sordellii 
##                                                              8 
##                                            Sergentomyia alderi 
##                                                              1 
##                                         Sergentomyia antennata 
##                                                              3 
##                                           Sergentomyia buxtoni 
##                                                              1 
##                                            Sergentomyia clydei 
##                                                              1 
##                                           Sergentomyia dentata 
##                                                              5 
##                                         Sergentomyia dreyfussi 
##                                                              2 
##                                             Sergentomyia dubia 
##                                                              1 
##                                            Sergentomyia fallax 
##                                                              2 
##                                             Sergentomyia magna 
##                                                              1 
##                                            Sergentomyia minuta 
##                                                             20 
##                                          Sergentomyia schwetzi 
##                                                              1 
##                                      Trichopygomyia longispina 
##                                                              1 
##                                           Uranotaenia balfouri 
##                                                              1 
##                                              Uranotaenia cooki 
##                                                              1 
##                                              Uranotaenia lowii 
##                                                              1 
##                                        Uranotaenia macfarlanei 
##                                                              1 
##                                         Uranotaenia sapphirina 
##                                                             18 
##                                        Uranotaenia unguiculata 
##                                                              6 
##                                            Verrallina carmenti 
##                                                              1 
##                                             Verrallina funerea 
##                                                              1 
##                                            Wyeomyia mitchellii 
##                                                              2
length(unique(w$VectorSpecies))
## [1] 687
head(w)
## # A tibble: 6 × 42
##   ID    First_Author Title    year Country `Region/State` `City/County` Latitude
##   <chr> <chr>        <chr>   <dbl> <chr>   <chr>          <chr>         <chr>   
## 1 2     Li           Invest…  2017 China   Yunnan provin… <NA>          "Sampli…
## 2 2     Li           Invest…  2017 China   Yunnan provin… <NA>          "Sampli…
## 3 2     Li           Invest…  2017 China   Yunnan provin… <NA>          "Sampli…
## 4 2     Li           Invest…  2017 China   Yunnan provin… <NA>          "Sampli…
## 5 2     Li           Invest…  2017 China   Yunnan provin… <NA>          "Sampli…
## 6 2     Li           Invest…  2017 China   Yunnan provin… <NA>          "Sampli…
## # ℹ 34 more variables: Longitude <dbl>, Continent <chr>, Year_Start <chr>,
## #   Year_End <chr>, Month_Start <chr>, Month_End <chr>,
## #   Continuous_or_annually <chr>, SamplingMethod <chr>, LifeStage <chr>,
## #   VectorGroup <chr>, VectorSpecies <chr>, VectorSpeciesOld <chr>,
## #   fedStatus <chr>, Host <chr>, anMethCode <chr>, MethodCategory <chr>,
## #   `N­Specimens­Tested` <dbl>, NPoolsTested <dbl>, Pool_size <chr>,
## #   `Positive/Negative` <chr>, NPoolspositive <chr>, VBD_Agent <chr>, …

4 Species specified on the Vector net output

species <- c("Aedes albopictus",
             "Aedes vexans vexans",
             "Aedes aegypti",
             "Aedes japonicus",
             "Culex pipiens",
             "Culex modestus", #MC: 28.11.2023 added
             "Culex tarsalis", ## not in the dataset
             "Culex quinquefasciatus") ## not in the dataset

table(w$VectorSpecies %in% species)
## 
## FALSE  TRUE 
##  5000   727

5 Number of reports for every country

reports <- w %>% 
  group_by(Country, Country_ISO) %>% 
  summarise(n(), diseases=length(unique(VBD_AS_Full)), vectorSP=length(unique(VectorSpecies)))
## `summarise()` has grouped output by 'Country'. You can override using the
## `.groups` argument.

5.1 Reading the World map

wm <- st_read("TM_WORLD_BORDERS_SIMPL-0.3.shp")
## Reading layer `TM_WORLD_BORDERS_SIMPL-0.3' from data source 
##   `C:\Users\alfredo.acosta\OneDrive - SVA\LORA\Working example\vectors\TM_WORLD_BORDERS_SIMPL-0.3.shp' 
##   using driver `ESRI Shapefile'
## Simple feature collection with 246 features and 11 fields
## Geometry type: MULTIPOLYGON
## Dimension:     XY
## Bounding box:  xmin: -180 ymin: -90 xmax: 180 ymax: 83.57027
## Geodetic CRS:  WGS 84

5.2 Number of reports on vectors (pop-up showing the number of on the map

  # WORLD MAP ----
  # Update the number of outbreaks on the map
  wm$reports <- reports$`n()`[match(wm$ISO2, reports$Country_ISO)]
  wm$diseases <- reports$diseases[match(wm$ISO2, reports$Country_ISO)]
  wm$vectors <- reports$vectorSP[match(wm$ISO2, reports$Country_ISO)]

  str(wm$reports)
##  int [1:246] 4 15 NA 11 6 NA NA 8 250 NA ...
# Maps of outbreaks
  pal <- colorNumeric(
    palette = "Spectral",
    domain = wm$reports, 
    na.color = "white"
  )


# Maps of cases ----
pal <- colorNumeric(
  palette = "Spectral",
   reverse = TRUE,
  domain = wm$reports, 
  na.color = "white")

map <- leaflet(wm) %>%
  addProviderTiles(providers$CartoDB.Positron)

mc <- map %>%
  setView(lng = 25, lat = 10, zoom = 2) %>%
  addPolygons(weight = 0.5, 
              color = ~pal(reports),
              popup = ~paste("Diseases:", diseases, "<br>", "Vectors", vectors)) %>% 
  addLegend("bottomright", pal = pal, values = ~reports,
            # title = paste("Cases",
            #               "<br>",
            #               date_to_analyse, 
            #               "<br>", 
            #               disease_to_analyse),
            opacity = 1)

mc

6 African Swine fever

reports <- w %>% 
  filter(VBD_Agent_subtype == "ASFV") %>% 
  group_by(Country, Country_ISO) %>% 
  summarise(n(), vector=length(unique(VectorSpecies)), vectorSP=paste(unique(VectorSpecies), collapse = ", "))
## `summarise()` has grouped output by 'Country'. You can override using the
## `.groups` argument.
reports
## # A tibble: 7 × 5
## # Groups:   Country [7]
##   Country      Country_ISO `n()` vector vectorSP                                
##   <chr>        <chr>       <int>  <int> <chr>                                   
## 1 China        CN             25     10 Culicoides homotomus, Culicoides obsole…
## 2 Malawi       MW            167      1 Ornithodoros moubata s.l.               
## 3 Mozambique   MZ             14      2 Ornithodoros porcinus porcinus, Ornitho…
## 4 Namibia      NA              1      1 Ornithodoros porcinus                   
## 5 South Africa ZA             18      8 Ornithodoros waterbergensis, Ornithodor…
## 6 Tanzania     TZ             11      2 Ornithodoros moubata s.l., Ornithodoros…
## 7 Zimbabwe     ZW              3      1 Ornithodoros porcinus

6.1 Map Number of reports on vectors (pop-up showing the name of on the map)

  # WORLD MAP ----
  # Update the number of outbreaks on the map
  wm$reports <- reports$`n()`[match(wm$ISO2, reports$Country_ISO)]
  wm$vector <- reports$vector[match(wm$ISO2, reports$Country_ISO)]
  wm$vectorSP <- reports$vectorSP[match(wm$ISO2, reports$Country_ISO)]

  str(wm$reports)
##  int [1:246] NA NA NA NA NA NA NA NA NA NA ...
# Maps of outbreaks
  pal <- colorNumeric(
    palette = "Spectral",
    domain = wm$reports, 
    na.color = "white"
  )


# Maps of cases ----
pal <- colorNumeric(
  palette = "Spectral",
   reverse = TRUE,
  domain = wm$reports, 
  na.color = "white")

map <- leaflet(wm) %>%
  addProviderTiles(providers$CartoDB.Positron)

mc <- map %>%
  setView(lng = 25, lat = 10, zoom = 2) %>%
  addPolygons(weight = 0.5, 
              color = ~pal(reports),
              popup = ~paste("N vectors:", vector, "<br>", "Names", vectorSP)) %>% 
  addLegend("bottomright", pal = pal, values = ~reports,
            # title = paste("Cases",
            #               "<br>",
            #               date_to_analyse, 
            #               "<br>", 
            #               disease_to_analyse),
            opacity = 1)

mc

7 West nile virus

reports <- w %>% 
  filter(VBD_Agent_subtype == "WNV") %>% 
  group_by(Country, Country_ISO) %>% 
  summarise(n(), vector=length(unique(VectorSpecies)), vectorSP=paste(unique(VectorSpecies), collapse = ", "))
## `summarise()` has grouped output by 'Country'. You can override using the
## `.groups` argument.
reports
## # A tibble: 32 × 5
## # Groups:   Country [32]
##    Country        Country_ISO `n()` vector vectorSP                             
##    <chr>          <chr>       <int>  <int> <chr>                                
##  1 Algeria        DZ              3      3 Culex perexiguus, Aedes caspius, Cul…
##  2 Austria        AT              2      1 Culex pipiens/torrentium             
##  3 Bulgaria       BG              1      1 Culex pipiens                        
##  4 Canada         CA             39     20 Culex pipiens/restuans, Culex salina…
##  5 China          CN              9      9 Culex tritaeniorhynchus, Anopheles s…
##  6 Cyprus         CY             30      3 Culex pipiens, Aedes detritus, Culex…
##  7 Czech Republic CZ             17      9 Aedes vexans, Aedes cinereus, Aedes …
##  8 France         FR              1      1 Ornithodoros maritimus               
##  9 Germany        DE             14      8 Aedes cinereus/geminus, Aedes japoni…
## 10 Greece         EL            125      4 Culex pipiens, Culex pipiens s.l., A…
## # ℹ 22 more rows

7.1 Map Number of reports on vectors (pop-up showing the name of on the map)

  # WORLD MAP ----
  # Update the number of outbreaks on the map
  wm$reports <- reports$`n()`[match(wm$ISO2, reports$Country_ISO)]
  wm$vector <- reports$vector[match(wm$ISO2, reports$Country_ISO)]
  wm$vectorSP <- reports$vectorSP[match(wm$ISO2, reports$Country_ISO)]

  str(wm$reports)
##  int [1:246] NA 3 NA NA NA NA NA NA NA NA ...
# Maps of outbreaks
  pal <- colorNumeric(
    palette = "Spectral",
    domain = wm$reports, 
    na.color = "white"
  )


# Maps of cases ----
pal <- colorNumeric(
  palette = "Spectral",
   reverse = TRUE,
  domain = wm$reports, 
  na.color = "white")

map <- leaflet(wm) %>%
  addProviderTiles(providers$CartoDB.Positron)

mc <- map %>%
  setView(lng = 25, lat = 10, zoom = 2) %>%
  addPolygons(weight = 0.5, 
              color = ~pal(reports),
              popup = ~paste("N vectors:", vector, "<br>", "Names", vectorSP)) %>% 
  addLegend("bottomright", pal = pal, values = ~reports,
            # title = paste("Cases",
            #               "<br>",
            #               date_to_analyse, 
            #               "<br>", 
            #               disease_to_analyse),
            opacity = 1)

mc

8 BTV

reports <- w %>% 
  filter(VBD_Agent_subtype == "BTV") %>% 
  group_by(Country, Country_ISO) %>% 
  summarise(n(), vector=length(unique(VectorSpecies)), vectorSP=paste(unique(VectorSpecies), collapse = ", "))
## `summarise()` has grouped output by 'Country'. You can override using the
## `.groups` argument.
reports
## # A tibble: 12 × 5
## # Groups:   Country [11]
##    Country     Country_ISO `n()` vector vectorSP                                
##    <chr>       <chr>       <int>  <int> <chr>                                   
##  1 Belgium     BE             34      6 Culicoides obsoletus complex, Culicoide…
##  2 China       CN             33     15 Culicoides homotomus, Culicoides obsole…
##  3 France      FR              1      1 Culicoides imicola                      
##  4 Germany     DE              5      2 Culicoides obsoletus group, Culicoides …
##  5 Italy       IT            110     12 Culicoides imicola, Culicoides newstead…
##  6 Italy       <NA>            7      6 Culicoides imicola, Culicoides obsoletu…
##  7 Japan       JP             12     12 Culicoides oxystoma, Culicoides tainanu…
##  8 Netherlands <NA>            9      5 Culicoides obsoletus complex, Culicoide…
##  9 Romania     RO             13      3 Culicoides obsoletus complex, Culicoide…
## 10 Russia      RU              2      2 Culicoides obsoletus complex, Culicoide…
## 11 Thailand    TH             15      5 Culicoides peregrinus, Culicoides orien…
## 12 USA         US             25      6 Culicoides crepuscularis, Culicoides de…

8.1 Map Number of reports on vectors (pop-up showing the name of on the map)

  # WORLD MAP ----
  # Update the number of outbreaks on the map
  wm$reports <- reports$`n()`[match(wm$ISO2, reports$Country_ISO)]
  wm$vector <- reports$vector[match(wm$ISO2, reports$Country_ISO)]
  wm$vectorSP <- reports$vectorSP[match(wm$ISO2, reports$Country_ISO)]

  str(wm$reports)
##  int [1:246] NA NA NA NA NA NA NA NA NA NA ...
# Maps of outbreaks
  pal <- colorNumeric(
    palette = "Spectral",
    domain = wm$reports, 
    na.color = "white"
  )


# Maps of cases ----
pal <- colorNumeric(
  palette = "Spectral",
   reverse = TRUE,
  domain = wm$reports, 
  na.color = "white")

map <- leaflet(wm) %>%
  addProviderTiles(providers$CartoDB.Positron)

mc <- map %>%
  setView(lng = 25, lat = 10, zoom = 2) %>%
  addPolygons(weight = 0.5, 
              color = ~pal(reports),
              popup = ~paste("N vectors:", vector, "<br>", "Names", vectorSP)) %>% 
  addLegend("bottomright", pal = pal, values = ~reports,
            # title = paste("Cases",
            #               "<br>",
            #               date_to_analyse, 
            #               "<br>", 
            #               disease_to_analyse),
            opacity = 1)

mc

9 MIR Mininum infection rates

9.1 Selection of pririotized diseases

# ASF   African Swine Fever
# CCHF  Crimean-Congo Haemorrhagic fever
# EHD   Epizootic Haemorrhagic Disease
# EE    Equine Encephalosis
# *** HPAI  Highly Pathogenic Avian Influenza
# JE    Japanese Encephalitis 
# *** LSD   Lumpy Skin Disease
# *** Rab   Rabies
# RVF   Rift Valley Fever
# WNF   West Nile Fever
# 
head(w)
## # A tibble: 6 × 42
##   ID    First_Author Title    year Country `Region/State` `City/County` Latitude
##   <chr> <chr>        <chr>   <dbl> <chr>   <chr>          <chr>         <chr>   
## 1 2     Li           Invest…  2017 China   Yunnan provin… <NA>          "Sampli…
## 2 2     Li           Invest…  2017 China   Yunnan provin… <NA>          "Sampli…
## 3 2     Li           Invest…  2017 China   Yunnan provin… <NA>          "Sampli…
## 4 2     Li           Invest…  2017 China   Yunnan provin… <NA>          "Sampli…
## 5 2     Li           Invest…  2017 China   Yunnan provin… <NA>          "Sampli…
## 6 2     Li           Invest…  2017 China   Yunnan provin… <NA>          "Sampli…
## # ℹ 34 more variables: Longitude <dbl>, Continent <chr>, Year_Start <chr>,
## #   Year_End <chr>, Month_Start <chr>, Month_End <chr>,
## #   Continuous_or_annually <chr>, SamplingMethod <chr>, LifeStage <chr>,
## #   VectorGroup <chr>, VectorSpecies <chr>, VectorSpeciesOld <chr>,
## #   fedStatus <chr>, Host <chr>, anMethCode <chr>, MethodCategory <chr>,
## #   `N­Specimens­Tested` <dbl>, NPoolsTested <dbl>, Pool_size <chr>,
## #   `Positive/Negative` <chr>, NPoolspositive <chr>, VBD_Agent <chr>, …
# Which abreviattion correspond to the disease
w %>% 
group_by(w$VBD_Agent_subtype, w$VBD_AS_Full) %>% 
  summarise(n())
## `summarise()` has grouped output by 'w$VBD_Agent_subtype'. You can override
## using the `.groups` argument.
## # A tibble: 27 × 3
## # Groups:   w$VBD_Agent_subtype [27]
##    `w$VBD_Agent_subtype` `w$VBD_AS_Full`                        `n()`
##    <chr>                 <chr>                                  <int>
##  1 AHFV                  Alkhurma haemorrhagic fever virus         13
##  2 AHSV                  African horse sickness virus              27
##  3 AKAV                  Akabane virus                             21
##  4 ASFV                  African swine fever virus                239
##  5 BTV                   Bluetongue virus                         266
##  6 CCHFV                 Crimean-Congo haemorrhagic fever virus   637
##  7 CVV                   Cache Valley virus                       120
##  8 CanL                  Leishmania infantum                      567
##  9 Cowdr                 Ehrlichia ruminantium                    174
## 10 EEEV                  Eastern equine encephalitis virus        118
## # ℹ 17 more rows
di <- c("ASFV","BTV","CCHFV", "EHDV", "EEV", "JEV", "RVFV", "WNV")

9.2 Options to filter

table(w$fedStatus)
## 
##                           Fed                 Fed and unfed 
##                           307                           227 
##                Fed or unknown                        Gravid 
##                            22                            30 
##             Gravid or unknown Gravid, semigravid, nongravid 
##                             8                             1 
##                        Parous              Parous or gravid 
##                             7                             9 
##                         Unfed 
##                           571
table(w$LifeStage)
## 
##                               Adult                                Eggs 
##                                1770                                   1 
## Eggs, larvae, pupae reared to adult                              Female 
##                                  37                                2887 
##                              Larvae                       Larvae, adult 
##                                  67                                  62 
##                       Larvae, nymph                Larvae, nymph, adult 
##                                   9                                  77 
##                                Male                               Nymph 
##                                 129                                 115 
##                        Nymph, adult 
##                                 235

9.3 Filtering criteria for Mosquitoes, Bitting midges and Sand flies (127)

a <- w %>% 
  filter(MIR > 0) %>% 
  # filter(VBD_Agent_subtype %in% di) %>%
  filter(fedStatus == "Unfed" | fedStatus == "Gravid") %>% 
  filter(VectorGroup == "Mosquitoes" | VectorGroup == "Biting midges" | VectorGroup == "Sand flies") %>%
  filter(LifeStage == "Female")

9.4 Filter criteria for Ticks (27)

b <-  w %>% 
    filter(MIR > 0) %>% 
    filter(fedStatus == "Unfed" | fedStatus == "Gravid") %>% 
    filter(VectorGroup == "Ticks")

9.5 Number of MIR values (Checking filter)

# Minimum infection rates
# After applying the filtering criteria on the feeding status and life stage, 42 MIR values were
# found or calculated for mosquitoes, 67 for sand flies, 27 for ticks, and 18 for biting midges.
# Records including MIR values are visualized in a boxplot grouped by vector group (Figure 4).
# Details per arthropod species are provided in Appendix F.

c <- rbind(a,b)
c %>% group_by(VectorGroup) %>% 
  summarise(n())
## # A tibble: 4 × 2
##   VectorGroup   `n()`
##   <chr>         <int>
## 1 Biting midges    18
## 2 Mosquitoes       42
## 3 Sand flies       67
## 4 Ticks            27

10 MIR Table

c <- rbind(a,b)

datatable(c %>% 
  filter(VBD_Agent_subtype %in% di) %>%
  group_by(VBD_AS_Full, VectorGroup) %>% 
  summarise(obs = n(),Min=round(min(MIR),2), Median=round(median(MIR),2), Max=round(max(MIR),2)))
## `summarise()` has grouped output by 'VBD_AS_Full'. You can override using the
## `.groups` argument.

10.1 MIR considerig disease, vector group and species

datatable(c %>% 
  filter(VBD_Agent_subtype %in% di) %>%
  group_by(VBD_AS_Full, VectorGroup, VectorSpecies) %>% 
  summarise(obs = n(),Min=round(min(MIR),2), Median=round(median(MIR),2), Max=round(max(MIR),2)))
## `summarise()` has grouped output by 'VBD_AS_Full', 'VectorGroup'. You can
## override using the `.groups` argument.

11 Boxplot of MIR - Disease

c %>% 
  filter(VBD_Agent_subtype %in% di) %>%
  group_by(VBD_AS_Full, VectorGroup) %>% 
  ggplot(aes(MIR, VBD_AS_Full)) +
  geom_boxplot()+
  labs(y = "Disease", x= "MIR %o")

11.1 Boxplot of MIR - Disease/VectorGroup

c %>% 
  filter(VBD_Agent_subtype %in% di) %>%
  group_by(VBD_AS_Full, VectorGroup, VectorSpecies) %>% 
  ggplot(aes(MIR, color=VBD_AS_Full, VectorGroup)) +
  geom_boxplot()+
  facet_grid(cols=vars(VBD_AS_Full), scales = "free")+
  theme(legend.position="none")+
  labs(y = "Disease", x= "MIR %o")

11.2 Boxplot of MIR - Disease/Species

c %>% 
  filter(VBD_Agent_subtype %in% di) %>%
  group_by(VBD_AS_Full, VectorGroup, VectorSpecies) %>% 
  ggplot(aes(MIR, color=VBD_AS_Full, VectorSpecies)) +
  geom_boxplot()+
  facet_grid(cols=vars(VBD_AS_Full), scales = "free")+
  theme(legend.position="none")+
  labs(y = "Disease", x= "MIR %o")

12 Credits

Acosta, Alfredo PhD1.

Swedish Veterinary Agency SVA1: SVA http://www.sva.se/.